---
author: Sam White
toc-title: Contents
toc-depth: 5
toc-location: left
layout: post
title: qPCR - C.gigas polyIC
date: '2023-07-26 11:42'
tags: 
  - qPCR
  - Crassostrea gigas
  - polyIC
  - CFX connect
categories: 
  - 2023
  - Miscellaneous
---
Using [cDNA from 20230721](https://robertslab.github.io/sams-notebook/posts/2023/2023-07-21-Reverse-Transcription---C.gigas-PolyIC-RNA/), performed qPCR on the following [primer sets selected by Steven](https://github.com/RobertsLab/resources/issues/1686) (GitHub Issue), along with `Cg_Actin` as a potential normalizing gene:

| SRID   | Primer              |
|--------|---------------------|
| 1170/1 | Cg_Actin            |
| 1830/1 | Cg_DICER            |
| 1172/3 | Cg_GAPDH            |
| 1832/3 | Cg_IRF2             |
| 1834/5 | Cg_SACSIN           |
| 1828/9 | Cg_VIPERIN          |
| 1826/7 | Cg_cGAS             |
| 1383/4 | Cg_citrate_synthase |

qPCR calcs:

- [20230726 - qPCR Calcs polyIC gigas cDNA](https://docs.google.com/spreadsheets/d/1yZYj3LSSEYbcXVd6PXT39CG9bsIX73LfnfqcaotHdH8/edit?usp=sharing) (Google Sheet)


Reactions were run on white, low-profile, 96-well qPCR plates (USA Scientific). A total of two plates were run. One was run on a CFC Connect (BioRad) and the other on a CFX96 (BioRad). See the qPCR Report in the [RESULTS](#results) section below for cycling params, plate layouts, etc.

All samples were run in _singular_. Normally duplicates/triplicates are run. However, due to time and sample constraints, samples were just run in _singular_. No template controls were run in duplicate.

---

# RESULTS

Brief note(s) on results:

- Samples `T2` and `T15` seem to come up earlier than all other samples in almost all of the primer sets.


qPCR Results file (CSV)

- [sam_2023-07-26_13-06-28_Connect-Quantification%20-Cq-Results.csv](https://owl.fish.washington.edu/Athaliana/qPCR_data/sam_2023-07-26_13-06-28_Connect-Quantification%20-Cq-Results.csv)

qPCR Data file (QPCRD - CFX Maestro required)

- [sam_2023-07-26_13-06-28_Connect.pcrd](https://owl.fish.washington.edu/scaphapoda/qPCR_data/cfx_connect_data/sam_2023-07-26_13-06-28_Connect.pcrd)

qPCR Report (PDF)

- [sam_2023-07-26_13-06-28_Connect.pdf](https://owl.fish.washington.edu/Athaliana/qPCR_data/qPCR_reports/sam_2023-07-26_13-06-28_Connect.pdf)


---

#### PLOTS

| SRID   | Primer              | Amplification Plot                                                                                                                                               | Melt Curve                                                                                                                                               |
|--------|---------------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------|
| 1170/1 | Cg_Actin            | ![Cg_Actin amplification plot](https://owl.fish.washington.edu/Athaliana/qPCR_data/sam_2023-07-26_13-06-28_Connect-Cg_Actin-amp-plots.png)                       | ![Cg_Actin melt plot](https://owl.fish.washington.edu/Athaliana/qPCR_data/sam_2023-07-26_13-06-28_Connect-Cg_Actin-melt-plots.png)                       |
| 1830/1 | Cg_DICER            | ![Cg_DICER amplification plot](https://owl.fish.washington.edu/Athaliana/qPCR_data/sam_2023-07-26_13-06-28_Connect-Cg_DICER-amp-plots.png)                       | ![Cg_DICER melt plot](https://owl.fish.washington.edu/Athaliana/qPCR_data/sam_2023-07-26_13-06-28_Connect-Cg_DICER-melt-plots.png)                       |
| 1172/3 | Cg_GAPDH            | ![Cg_GAPDH amplification plot](https://owl.fish.washington.edu/Athaliana/qPCR_data/sam_2023-07-26_13-06-28_Connect-Cg_GAPDH-amp-plots.png)                       | ![Cg_GAPDH melt plot](https://owl.fish.washington.edu/Athaliana/qPCR_data/sam_2023-07-26_13-06-28_Connect-Cg_GAPDH-melt-plots.png)                       |
| 1832/3 | Cg_IRF2             | ![Cg_IRF2 amplification plot](https://owl.fish.washington.edu/Athaliana/qPCR_data/sam_2023-07-26_13-06-28_Connect-Cg_IRF2-amp-plots.png)                         | ![Cg_IRF2 melt plot](https://owl.fish.washington.edu/Athaliana/qPCR_data/sam_2023-07-26_13-06-28_Connect-Cg_IRF2-melt-plots.png)                         |
| 1834/5 | Cg_SACSIN           | ![Cg_SACSIN amplification plot](https://owl.fish.washington.edu/Athaliana/qPCR_data/sam_2023-07-26_13-06-28_Connect-Cg_SACSIN-amp-plots.png)                     | ![Cg_SACSIN melt plot](https://owl.fish.washington.edu/Athaliana/qPCR_data/sam_2023-07-26_13-06-28_Connect-Cg_SACSIN-melt-plots.png)                     |
| 1828/9 | Cg_VIPERIN          | ![Cg_VIPERIN amplification plot](https://owl.fish.washington.edu/Athaliana/qPCR_data/sam_2023-07-26_13-06-28_Connect-Cg_VIPERIN-amp-plots.png)                   | ![Cg_VIPERIN melt plot](https://owl.fish.washington.edu/Athaliana/qPCR_data/sam_2023-07-26_13-06-28_Connect-Cg_VIPERIN-melt-plots.png)                   |
| 1826/7 | Cg_cGAS             | ![Cg_cGAS amplification plot](https://owl.fish.washington.edu/Athaliana/qPCR_data/sam_2023-07-26_13-06-28_Connect-Cg_cGAS-amp-plots.png)                         | ![Cg_cGAS melt plot](https://owl.fish.washington.edu/Athaliana/qPCR_data/sam_2023-07-26_13-06-28_Connect-Cg_cGAS-melt-plots.png)                         |
| 1383/4 | Cg_citrate_synthase | ![Cg_citrate_synthase amplification plot](https://owl.fish.washington.edu/Athaliana/qPCR_data/sam_2023-07-26_13-06-28_Connect-Cg_citrate_synthase-amp-plots.png) | ![Cg_citrate_synthase melt plot](https://owl.fish.washington.edu/Athaliana/qPCR_data/sam_2023-07-26_13-06-28_Connect-Cg_citrate_synthase-melt-plots.png) |